How to use

getCommand

method

in

org.renci.common.exec.CommandInput

    : sourceFileSB.toString(), input.getWorkDir().getAbsolutePath(), input.getCommand());
try {
  wrapperFile = File.createTempFile("shellwrapper-", ".sh", input.getWorkDir());
    env = environmentToArray(input.getEnvironment());
  logger.info("running command: {}", input.getCommand());
  process = runtime.exec(wrapperFile.getAbsolutePath(), env, input.getWorkDir());

logger.debug("ci.getCommand(): {}", ci.getCommand());
commandOutput = executor.execute(ci, mapseqrc);
logger.info("commandOutput.getExitCode(): {}", commandOutput.getExitCode());